Reef manta rays (Manta alfredi) are a valuable ecotourism commodity in many areas of the world. Despite their value and threatened species listing, much remains unknown with regards to local population sizes and movements. Reef manta rays predictably aggregate at known sites seasonally, allowing for photographic mark-recapture, biopsy and tagging. Currently, estimation of reef manta ray population size and movement relies largely on long term mark-recapture photographic databases. Molecular genetic approaches provide a unique conservation tool for the study of threatened marine species. Not only can they provide estimates of genetic effective population size (Ne), they can offer additional insight into critical parameters for threatened species management, such as population structure and connectivity. In this study, we are using 10 microsatellite loci to investigate the population genetic structure of reef manta rays from three locations of ecotourism value around Australia. Small tissue biopsies were obtained from manta rays at Lady Elliot Island and Stradbroke Island in Queensland, and from Coral Bay in Western Australia. Hypotheses of connectivity between locations were derived from the known photographic movement history for each individual. Preliminary results will be presented testing for significant differences in populations of manta rays on the East and West coasts of Australia and between two photo ID-connected populations on the East coast. Although this study is ongoing, preliminary results emphasise the importance and value of molecular genetic approaches.